The Non-Growth Associated Maintenance reaction (NGAM) is an ATP-hydrolysis reaction added to metabolic models to represent energy expenses that the cell invests in continuous processes independent of the growth rate. Memote tries to infer this reaction from a list of buzzwords, and the stoichiometry and components of a simple ATP-hydrolysis reaction. Implementation: From the list of all reactions that convert ATP to ADP select the reactions that match the irreversible reaction "ATP + H2O -> ADP + HO4P + H+", whose metabolites are situated within the main model compartment. The main model compartment is assumed to be the cytosol, yet, if that cannot be identified, it is assumed to be the compartment with the most metabolites. The resulting list of reactions is then filtered further by attempting to match the reaction name with any of the following buzzwords ('maintenance', 'atpm', 'requirement', 'ngam', 'non-growth', 'associated'). If this is possible only the filtered reactions are returned, if not the list is returned as is.

A total of 1 NGAM reactions could be identified: ATPM

Universally blocked reactions are reactions that during Flux Variability Analysis cannot carry any flux while all model boundaries are open. Generally blocked reactions are caused by network gaps, which can be attributed to scope or knowledge gaps. Implementation: Use flux variability analysis (FVA) implemented in cobra.flux_analysis.find_blocked_reactions with open_exchanges=True. Please refer to the cobrapy documentation for more information: https://cobrapy.readthedocs.io/en/stable/autoapi/cobra/flux_analysis/ variability/index.html#cobra.flux_analysis.variability. find_blocked_reactions

There are 215 (18.99%) blocked reactions in the model: HYDA, PPBNGS, HMBS, ADMDC, GTHPi, ...